Selective resonance of chemical structures

ABSTRACT

Chemical compositions may be selectively or preferentially excited by the application of scores comprising a series of at least four differing energy inputs. The differing energy inputs of the specified series are selected to resonate each of a group of resonant structures among a group of proximate atoms, including at least one bond.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is related to, claims the earliest availableeffective filing date(s) from (i.e., claims earliest available prioritydates for other than provisional patent applications; claims benefitsunder 35 USC §119(e) for provisional patent applications), andincorporates by reference in its entirety all subject matter of thefollowing listed application(s) (the “Related Applications”) to theextent such subject matter is not inconsistent herewith; the presentapplication also claims the earliest available effective filing date(s)from, and also incorporates by reference in its entirety all subjectmatter of any and all parent, grandparent, great-grandparent, etc.applications of the Related Application(s) to the extent such subjectmatter is not inconsistent herewith. The United States Patent Office(USPTO) has published a notice to the effect that the USPTO's computerprograms require that patent applicants reference both a serial numberand indicate whether an application is a continuation orcontinuation-in-part. The present applicant entity has provided below aspecific reference to the application(s) from which priority is beingclaimed as recited by statute. Applicant entity understands that thestatute is unambiguous in its specific reference language and does notrequire either a serial number or any characterization such as“continuation” or “continuation-in-part.” Notwithstanding the foregoing,applicant entity understands that the USPTO's computer programs havecertain data entry requirements, and hence applicant entity isdesignating the present application as a continuation-in-part of itsparent applications, but expressly points out that such designations arenot to be construed in any way as any type of commentary and/oradmission as to whether or not the present application contains any newmatter in addition to the matter of its parent application(s).

RELATED APPLICATIONS

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of currently co-pendingU.S. patent application Ser. No. 11/186,632, filed Jul. 21, 2005entitled SELECTIVE RESONANCE OF CHEMICAL STRUCTURES, naming Muriel Y.Ishikawa, Edward K.Y. Jung, Nathan P. Myhrvold, and Lowell L. Wood, Jr.as inventors, filed contemporaneously herewith.

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of currently co-pendingU.S. patent application Ser. No. 11/186,394, entitled SELECTIVERESONANCE OF CHEMICAL STRUCTURES, naming Muriel Y. Ishikawa, Edward K.Y.Jung, Nathan P. Myhrvold, and Lowell L. Wood, Jr. as inventors, filedJul. 21, 2005 contemporaneously herewith.

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of currently U.S. patentapplication Ser. No. 11/186,633, now U.S. Pat. No. 7,979,213 entitledSELECTIVE RESONANCE OF CHEMICAL STRUCTURES, naming Muriel Y. Ishikawa,Edward K. Y. Jung, Nathan P. Myhrvold, and Lowell L. Wood, Jr. asinventors, filed Jul. 21, 2005 contemporaneously herewith.

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of currently co-pendingU.S. patent application Ser. No. 11/186,634, entitled SELECTIVERESONANCE OF CHEMICAL STRUCTURES, naming Muriel Y. Ishikawa, Edward K.Y.Jung, Nathan P. Myhrvold, and Lowell L. Wood, Jr. as inventors, filedJul. 21, 2005 contemporaneously herewith.

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of currently co-pendingU.S. patent application Ser. No. 11/186,631, entitled SELECTIVERESONANCE OF CHEMICAL STRUCTURES, naming Muriel Y. Ishikawa, Edward K.Y.Jung, Nathan P. Myhrvold, and Lowell L. Wood, Jr. as inventors, filedJul. 21, 2005 contemporaneously herewith.

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of currently co-pendingU.S. patent application Ser. No. 11/186,912, entitled SELECTIVERESONANCE OF CHEMICAL STRUCTURES, naming Muriel Y. Ishikawa, Edward K.Y.Jung, Nathan P. Myhrvold, and Lowell L. Wood, Jr. as inventors, filedJul. 21, 2005 contemporaneously herewith.

SUMMARY

In one aspect, a method of applying energy to a selected group ofproximate atoms within a medium comprises selecting a score specifying aseries of differing energy inputs, and applying the series of differingenergy inputs specified by the score to the medium. As will be describedfurther herein, the term “differing” is not necessarily restricted toenergy inputs from different source mechanisms, energy inputs atdifferent frequencies, or temporally or spatially non-overlapping energyinputs.

The differing energy inputs of the series are selected to resonate eachresonant structure of a plurality of resonant structures among the groupof proximate atoms. The score may be selected so that applying theseries of differing energy inputs has a physical effect, such astransferring substantially more energy to at least a portion of thegroup of proximate atoms than to other atoms in the medium, breaking apredetermined bond between two members of the group of proximate atoms,or changing a kinetic parameter of a reaction involving a member of thegroup of proximate atoms. Energy transfer to the medium may bepredominantly through resonant excitation of the plurality of resonantstructures. The plurality of resonant structures may be resonatedsimultaneously, sequentially, and/or in a temporally overlappingfashion. The series of differing energy inputs may be appliedsimultaneously, sequentially, and/or in a temporally overlappingfashion.

The group of proximate atoms may form at least a portion of a molecule(e.g., a biomolecule such as a protein or nucleotide), at least aportion of a crystal, or at least a portion of a complex of molecules.Members of the group of proximate atoms in some cases may be separatedby a distance of no more than 300 Å, and/or may be connected directly orindirectly by bonds between the atoms (e.g., covalent, ionic, metallic,van der Waals, hydrogen, coulombic, and/or magnetic attractions). Thescore may comprise at least 4, at least 10, or at least 36 energyinputs. The plurality of resonant structures may comprise a longitudinalvibrational mode of a bond, a bending mode of two bonds, and/or asquashing mode of a plurality of bonds between members of the group ofproximate atoms.

The score may specify application of one or more electromagnetic beamsas energy input(s), which may have a characteristic selected from thegroup consisting of a selected set of frequencies, a selected set ofmodulation frequencies, a selected set of phases, a selected set ofamplitudes, a selected temporal profile, a selected set ofpolarizations, and a selected direction. The selected set of frequenciesand/or the selected set of modulation frequencies may be approximatelymonochromatic, may comprise a plurality of local maxima, and/or maycomprise two frequencies having differing amplitudes. Theelectromagnetic beam may be coherent or incoherent. The temporal profilemay be characterized by a selected beam duration, and/or by a selectedchange in frequency, modulation frequency, phase, amplitude,polarization, or direction during a selected time interval. Theelectromagnetic beam may be polarized, amplitude modulated, or frequencymodulated, and it may be, for example, an infrared beam. A plurality ofelectromagnetic beams may differ in frequency, modulation frequency,phase, amplitude, polarization, or direction, and/or may intersect at atarget location. The method may include scanning the electromagneticbeam.

The method may also include applying a field to the medium, the fieldpreferentially orienting at least a portion of the group of proximateatoms. The field may be, for example, an electric field, a magneticfield, an electromagnetic field, a mechanical stress, a mechanicalstrain, a lowered or elevated temperature, a lowered or elevatedpressure, a phase change, an adsorbing surface, a catalyst, an energyinput, or a combination of any of these.

The plurality of resonant structures may be in an arrangement having twoend resonant structures and a center resonant structure, and may beresonated in a sequence beginning from the two end resonant structuresand progressing towards the center resonant structure (which may be atemporally overlapping sequence). The group of proximate atoms mayundergo a physical effect upon resonance of the center structure. Theresonance of the center structure may break a predetermined bond betweentwo members of the group of proximate atoms.

In another aspect, a method of exciting a composition including aplurality of resonant structures, each having a resonant frequency,comprises selecting a set of excitation energies and applying the set ofexcitation energies to the composition. Each excitation energy has afrequency (e.g., a modulation frequency) matching the resonant frequencyof at least one of the resonant structures. Together, the excitationenergies cause a chemical change in the composition that would not becaused by the application of any one of the excitation energies appliedalone. The excitation energies may be applied simultaneously,sequentially, or in a temporally overlapping fashion. The chemicalchange in the composition may include, for example, breaking a bondbetween two atoms of the composition and/or changing a kinetic parameterof a reaction involving the composition. The composition may be abiomolecule (e.g., a protein or nucleotide), a crystal, or a complex ofmolecules. The set of excitation energies may comprise at least 4, atleast 10, or at least 36 excitation energies. The plurality of resonantstructures may comprise a longitudinal vibrational mode of a bond, abending mode of two bonds to an atom, and/or a squashing mode of aplurality of bonds.

The excitation energies may be electromagnetic beams, each of which mayhave at least one characteristic selected from the group consisting of aselected set of frequencies, a selected set of phases, a selected set ofamplitudes, a selected temporal profile, a selected set ofpolarizations, and a selected direction. The selected set of frequenciesmay be monochromatic, may comprise a plurality of local maxima, may beGaussian, or may comprise at least two frequencies having differingamplitudes. At least one of the electromagnetic beams may be coherent orincoherent. The temporal profile may be characterized by a selected beamduration, and/or by a selected change in frequency, modulationfrequency, phase, amplitude, polarization, or direction during aselected time interval. At least one electromagnetic beam may bepolarized, amplitude modulated, or frequency modulated, and it may be,for example, an infrared beam. A plurality of electromagnetic beams maydiffer in frequency, modulation frequency, phase, amplitude,polarization, or direction, and/or may intersect at a target location.The method may include scanning at least one electromagnetic beam.

The method may also include applying a field to the medium, the fieldpreferentially orienting at least a portion of the group of proximateatoms. The field may be, for example, an electric field, a magneticfield, an electromagnetic field, a mechanical stress, a mechanicalstrain, a lowered or elevated temperature, a lowered or elevatedpressure, a phase change, an adsorbing surface, a catalyst, an energyinput, or a combination of any of these.

The plurality of resonant structures may be in an arrangement having twoend resonant structures and a center resonant structure, and may beresonated in a sequence beginning from the two end resonant structuresand progressing towards the center resonant structure (which may be atemporally overlapping sequence). The composition may undergo a physicaleffect upon resonance of the center structure. The resonance of thecenter structure may break a predetermined bond between two atoms of thecomposition.

In yet another aspect, a method of selectively exciting resonantstructures in a material comprises applying a first excitation energy tothe material to excite a first resonant structure, thereby shifting aresonant frequency of a second resonant structure, and applying a secondexcitation energy to the material to excite the second resonantstructure at its shifted resonant frequency. In some cases, theexcitation of the second resonant structure at its shifted resonantfrequency may shift a resonant frequency of a third resonant structure,and the method may include applying a third excitation energy to thematerial to excite the third resonant structure at its shifted resonantfrequency. The method may also include analogous shifting and excitingof at least 8 additional resonant structures, or of at least 34additional resonant structures, at their respective shifted resonances.The first and second resonant structures may be at least portions of amolecule (e.g., a biomolecule such as a protein or a nucleotide), acrystal, or a complex of molecules. The first and second resonantstructures may be longitudinal vibrational modes of two adjacent bonds,or of two nonadjacent bonds. At least one of the first and secondresonant structures may comprise at least two bonds, and/or may be abending mode or a squashing mode.

At least one of the first and second excitation energies may be anelectromagnetic beam (e.g., an infrared beam), which may be amplitudemodulated or frequency modulated. The method may include scanning thebeam. At least one of the first and second excitation energies may be aplurality of electromagnetic beams, which may differ in polarization ororientation, and which may intersect at a target location.

In still another aspect, a method of characterizing a compositioncomprises determining a score specifying a series of differing energyinputs, and identifying the composition by the determined score. Thediffering energy inputs of the specified series are selected to resonateeach resonant structure, and application of the differing energy inputsselectively affects the composition. The score may have a physicaleffect on the composition such as transferring substantially more energyto the composition than to other material to which the set of differingenergy inputs is applied, breaking a predetermined bond between twoatoms of the composition, and/or changing a kinetic parameter of areaction involving the composition. The score may be determined, forexample, by determining resonant frequencies by computational modelingor by spectroscopy, and/or by applying a plurality of sets of energyinputs to the composition and observing their effects. The method mayfurther include applying the set of energy inputs to the composition.The composition may be a biomolecule, such as a nucleotide or a protein,and the score may specify as many as 4, 10, or 36 energy inputs.

In a further aspect, a method of characterizing a target molecule orgroup of molecules in an environment comprises identifying a group ofresonant structures within the target and determining a score specifyinga set of applied frequencies. Each resonant structure in the grouppossesses at least one characteristic resonant frequency, thecharacteristic resonant frequency of a shiftable resonant structure inthe group can be shifted by exciting a shifting resonant structure inthe group, and the group of resonant structures is substantially absentfrom nontarget molecules in the environment. The applied frequencies ofthe score, when applied in sequence to the target, shift thecharacteristic resonant frequency of the shiftable resonant structurethrough excitation of the shifting resonant structure, excite theshiftable resonant structure at its shifted resonant frequency, andselectively change the energy or state of at least a portion of thetarget relative to its environment. The method may further compriseapplying the set of applied frequencies to the environment of the targetmolecule. The set of applied frequencies, when applied in sequence tothe target, shift the resonance of and excite a plurality of theresonant structures at their respective shifted resonances. Determininga set of applied frequencies may include computational modeling of thetarget, spectroscopically observing the target, and/or applying aplurality of sets of applied frequencies to the environment andobserving their effects on the target. The target may comprise abiomolecule (e.g., a nucleotide or a protein). The identified group ofresonant structures may include as many as 4, 10, or 36 resonantstructures, and/or may be contiguous within a molecule. The shiftableresonant structure and the shifting resonant structure may or may notshare an atom.

In a still further aspect, an instrument for determining a scorespecifying a series of energy inputs having a physical effect on atarget composition includes a test score generator, an energy inputcomponent, and a monitor. The test score generator selects a test scorefor application to the target composition. The energy input componentapplies the energy inputs specified by the test score to the targetcomposition. The monitor tests whether the target composition has beenphysically affected by the application of the energy inputs specified bythe test score. The test score may comprise a set of energy inputdescriptors, each descriptor specifying frequency, modulation frequency,phase, amplitude, temporal profile, polarization, direction, and/orcoherence. The test score generator may select a test score using aspectroscopic profile of the specimen, molecular modeling, a database ofscores, and/or feedback from the monitor. The monitor may measure aproperty of the target composition such as energy levels, kineticeffects, structural changes, chemical activities, index of refraction,diffraction properties, optical absorption, and/or temperature, and mayinclude a thermal imager and/or a sensor that monitors an optical beamdirected at the target composition.

In yet a further aspect, a blood therapy device comprises an energyinput component adapted to be placed on or in a human or animal body.The energy input component directs a set of differing energy inputstowards a blood vessel, wherein they selectively resonate a plurality ofresonant structures in a target composition in the blood. The bloodtherapy device may also include a monitor that observes effects of theresonance of the plurality of resonant structures. The resonance maymodify or destroy the target composition (e.g., a virus, a biomoleculesuch as a protein, sugar, triglyceride, or cholesterol, and/or apharmaceutical such as heparin). The energy input component may directthe set of differing energy inputs through the skin, and/or via animplanted energy transmission device such as an optical fiber.

In an additional aspect, an instrument for determining a scorespecifying a series of energy inputs having a physical effect on atarget composition comprises a modeling tool and a score generator. Themodeling tool computationally determines resonant properties of thetarget composition based on its molecular structure and identifies aseries of energy inputs expected to selectively resonate resonantstructures of the target composition. The score generator creates adescriptor of the identified series of energy inputs, specifyingfrequency, modulation frequency, phase, amplitude, temporal profile,polarization, direction, and/or coherence. The descriptor is readable byan instrument for applying the identified series of energy inputs to acomposition.

In a further aspect, a chemical agent for therapeutic use comprises acomposition having a characteristic set of proximate bonds selectivelyresponsive to a predetermined series of energy inputs. The response ofthe composition to the predetermined series of energy inputs is selectedfrom the group consisting of breaking one or more bonds of thecomposition, ablating material surrounding the composition, heatingmaterial surrounding the composition, and reacting with materialsurrounding the composition. The chemical agent may have an affinity fora selected substance or tissue in vivo, or be bound to a carrier havinga similar affinity. The predetermined series of energy inputs mayinclude an energy input at a frequency to which living tissue issubstantially transparent, which may be, for example, frequencymodulated or amplitude modulated. The energy inputs may be appliedsimultaneously, sequentially, and/or in a temporally overlappingfashion, and the series may comprise as many as 4, 10, or 36 energyinputs.

A method of introducing an agent to a selected tissue may includeplacing the chemical agent in an animal or human body comprising theselected tissue and applying the score to the body. For example, thechemical agent may be introduced by injection into the tissue, byintroduction into the body (e.g., orally, by injection into thebloodstream or the lymphatic system, or by inhalation) and accumulationat the tissue, and/or by placing a carrier bound to the chemical agentin the body. Application of the score may cause the chemical agent toablate the surrounding tissue.

In yet another aspect, a library of excitation energy specificationsincludes a structured data repository comprising a plurality of scorerecords. Each score record comprises descriptors for a plurality ofenergy inputs and a descriptor for an associated composition affected bythe plurality of energy inputs, each energy input descriptor specifyingfrequency, modulation frequency, phase, amplitude, temporal profile,polarization, and/or direction. The library may also include a searchengine that allows a user to search for a score record, for example bycomposition, chemical structure, or energy input descriptor. The librarymay also include an input component that allows a user to add a scorerecord to the structured data repository, or an output component thatallows a user to download a score record. The energy input descriptorsand/or the score records may be stored in a tagged data file format suchas XML. The score records may also comprise a descriptor describing theeffect of the plurality of energy inputs on the composition.

A method of screening for a composition in a medium may compriseaccessing the library to locate a score for the composition, applyingthe energy inputs described by the energy descriptors of the locatedscore to the medium, and observing the medium for reaction of thecomposition to the applied energy inputs. A method of exciting acomposition in a medium may comprise accessing the library to locate ascore for the composition and applying the energy inputs of the locatedscore to the medium, wherein the effect of the plurality of energyinputs is to excite the composition. This excitation may destroy thecomposition.

In yet another aspect, a method of resonating a selected composition ina medium includes accessing a database of score records, selecting ascore record from the database, and applying a series of differingenergy inputs from the score record to the medium. Each score record ofthe database specifies a series of differing energy inputs and acomposition comprising a plurality of resonant structures, the differingenergy inputs of the series being selected to resonate each resonantstructure of the plurality of resonant structures of the composition. Ascore record may specify a plurality of compositions. The selected scorerecord may specify the selected composition, or may specify acomposition having a common functional group with the selectedcomposition.

In yet still a further aspect, an instrument for exciting chemicalcompositions may include an interpreter, and an energy input component(e.g., a laser). The interpreter converts a score comprising a pluralityof energy input descriptors into control instructions for the energyinput component, which directs energy input into a medium in accordancewith the generated control instructions. Each energy descriptor mayinclude a description of frequency, modulation frequency, phase,amplitude, temporal profile, polarization, direction, and/or coherence.The energy input component may include a beam control element (e.g., areflector, a polarizer, an optical fiber, and/or a lens) that directs ormodifies the beam. The instrument may also include a score locationcomponent that selects a score to be converted by the interpreter. Thescore location component may select the score from a library of scores,each score of the library being associated with one or more compositionsupon which the score has a physical effect. Scores from the library mayinclude a descriptor of the physical effect, and the library may beremote from the energy input component. The interpreter may include acontroller that receives the score from a source. The instrument mayalso include a monitor in communication with the controller, and thecontroller may adjust the score converted by the interpreter in responseto an observation by the monitor.

The instrument may also include an input component that allows a user tospecify a score to be converted by the interpreter, and/or an inputcomponent that allows a user to specify a composition or structure and alookup component that determines a score that describes a set of energyinputs having a physical effect on the specified composition orstructure and passes the determined score to the interpreter forconversion. The lookup component may access a library of scoresassociated with composition(s), which may be remote from the energyinput component. The lookup component may present the score to the userfor approval (e.g., visually or audibly) before passing it to theinterpreter. Audible presentation may include mapping energy inputfrequencies to audible frequencies for playback to the user.

In still a further aspect, a method of communicating score informationto a user comprises selecting a first score comprising a first pluralityof energy input descriptors, applying a selected mapping of the firstplurality of energy input descriptors to a first plurality ofuser-perceivable signals, and presenting the first plurality ofuser-perceivable signals to the user. The energy input descriptorscomprise an attribute description of frequency, modulation frequency,phase, amplitude, temporal profile, polarization, direction, and/orcoherence. The selected mapping may include mapping the attributedescription to an audible tone (e.g., mapping energy frequency to tonefrequency, energy duration to tone duration, and/or any attribute totimbre). The selected mapping may also or alternatively include mappingthe attribute description to a visible signal (e.g., mapping energyfrequency to a visible color, energy duration to a display location,and/or any attribute to shape). The method may further include selectinga second score, applying the mapping from the second plurality of energyinput descriptors to a second plurality of user-perceivable signals, andpresenting the second plurality of user-perceivable signals to a user(e.g., concurrently with the presentation of the first plurality ofuser-perceivable signals).

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A, 1B, and 1C illustrate longitudinal, bending, and squashingmodes, respectively, of resonant structures.

FIG. 2 is a schematic representation of a four-note score.

FIG. 3 illustrates how a frequency of one resonant structure may shiftas another resonant structure is excited.

FIG. 4 is a schematic representation of the response of a molecule to aseries of energy inputs.

FIG. 5 illustrates diagrammatically excitation to breakage of a bond ina linear molecule.

FIG. 6 illustrates diagrammatically the application of multipleintersecting energy inputs to a target voxel.

FIG. 7 is a schematic showing the application of an electric field toalign resonant structures in a medium.

FIG. 8 is a schematic representation of an energy application method.

FIG. 9 is a schematic representation of a device for applying energyaccording to a score.

FIG. 10 is a schematic representation of a device with optionalmonitoring and feedback control for score application.

FIG. 11 is a schematic representation of an apparatus for generatingscore.

FIG. 12 illustrates a system for introducing a chemical agent into amedium.

FIG. 13 is a schematic representation of a library of excitation energyspecifications.

DETAILED DESCRIPTION

The term “biomolecule,” as used herein, includes without limitationproteins, peptides, amino acids, nucleotides, nucleic acids,carbohydrates, sugars, glycoproteins, lipids, viruses, prions,antibodies, and enzymes, and fragments, derivatives, and modified formsof any of these, and any other naturally-occurring or synthetic moleculeor complex of molecules that has a biological activity or that iseffective in modulating a biological activity.

The term “bond,” as used herein, includes without limitation covalent,ionic, metallic, van der Waals, hydrogen, coulombic, and magneticattractions, as well as any other attractive force between atoms orother particles.

Resonant structures of molecules, crystals, and other compositions haveone or more characteristic resonant frequencies, at which theyrelatively efficiently absorb or otherwise interact with energy appliedat matching frequencies. Spectroscopic techniques exploit thesecharacteristic resonances to extract information about chemicalstructure and properties. For example, covalent bonds typically have acharacteristic frequency of longitudinal vibration which depends insignificant part upon the masses of the atoms forming the bond and thestrength of the bond (e.g., single, double, triple, etc). FIG. 1A showsa single covalent bond between atoms B and C, which may vibrate in sucha longitudinal mode. Vibration of ionic bonds is similarly affected bythe mass, atomic radius, and charge of the atoms involved. Resonantstructures may also be formed by groups of bonds, e.g., in bending orsquashing modes (shown in FIGS. 1B and 1C, respectively), each with itsown characteristic resonant frequency or frequencies. Crystals mayexhibit resonances based on their periodic structures or otherproperties. Molecule complexes may have resonances that include hydrogenbonds or other attractions between molecules of the complex. Thecharacteristic frequencies of any of these structures may be shifted bya wide variety of factors, including without limitation the propertiesof adjacent bonds, the excitation state of the molecule or crystal, thepresence of defects in a crystal (e.g., free surfaces that cause theresonant properties of “quantum dot” crystallites to depend on theirsize), stresses in the structure, electric or magnetic fields, or otherfactors that may influence the properties of the structure. Spectroscopyinvolves directing energy at a target, and examining the absorbed,transmitted, reflected, and/or emitted frequency spectrum tocharacterize the physical properties of the target.

Methods are provided herein for directing energy inputs into a target tomanipulate or otherwise interact selectively with its structures. Inparticular, a set of energy inputs analogous to a musical score may beidentified, where different “notes” of the score transfer energy withspatio-temporal selectivity to a target composition, for example byresonating different resonant structures. For scores having a sufficientnumber of notes, high specificity may be obtained, for example whereincompositions having all or most of the corresponding resonant structuresare preferentially excited by “playing the score” to the targetcomposition. Even for “short” scores, energy may be efficientlytransmitted to a target composition that matches most or all of theresonances identified by the score. Notes as used in this descriptionare not limited to representations of frequency. Notes may alsorepresent, without limitation, amplitudes, polarizations, phasecomponents, gradients, or other characteristics of input energies. Whileresonance is an exemplary method of transferring energy that can providespatio-temporal control or other selectivity as discussed below, scoresmay also include energy inputs that transfer energy to molecules in anonresonant fashion. For example one or more optical beams, coherentoptical pulses, or other controllable inputs can transfer energyselectively to particular portions of a molecule and/or at particulartimes.

In one aspect, the scores may be used to characterize or identifycompositions, as an alternative nomenclature to conventional chemicalcomposition and structure notation. Digital or analog processing,visually presenting, or otherwise processing or treating the scores mayindicate or reveal into similarities between compositions that are lessreadily identified using conventional nomenclature.

Scores having desired effects on particular compositions may bedetermined by a variety of methods. One starting point for determining ascore may be to examine a spectrogram of a composition of interest,since the spectrogram reflects certain resonant responses of thecomposition. Alternatively, resonances may be calculated bycomputational methods. Scores may also be determined and/or refined onan empirical basis, using “trial and error” approaches, inferentialapproaches, observations of trends or other empirical approaches.Typically, such approaches would include applying a candidate score, aportion of a candidate score, or a selected set of notes to acomposition and observing the corresponding effects, such as energyabsorption, polarization changes, chemical reactions, opticalcharacteristics, vibrations, stresses, changes in electrical or magneticproperties, or other effects. The score, portion of a score, or notesmay be applied at an amplitude level that may differ from the level tobe used in applying the determined score at a later time. For example, asample note may be applied at a significantly higher amplitude as partof the characterization than may be appropriate for later applications.

Scores may have a diverse set of potential effects on variouscompositions. A score may resonate a particular bond in a molecule tobreakage, for example, or it may change a kinetic parameter of anaffected composition or cause local heating in the vicinity of thecomposition. In some embodiments, the scores can act as a form of energycatalyst, preferentially shifting the kinetics of selected chemicalreactions. For example, a score could alter the kinetics of achromatography column, causing a reactant to bind or to unbind inresponse to an applied score. Similarly, a score may alter the migrationrate of composition during an electrophoresis process. In this approach,the score may be used to separate stereoisomers during electrophoresis.

Other embodiments include selectively destroying a contaminant or otherunwanted composition, such as removing an undesirable metabolic product(e.g., beta-amyloid plaques in Alzheimer's disease patients, gallstones,or kidney stones), a contaminant (e.g., accumulations of tobacco residuein the lungs), a therapeutic agent not desirable for long-term use(e.g., heparin from the blood of dialysis patients downstream of thedialysis unit), or cell type (e.g., cancerous cells) from living tissue,breaking down pollutants in a smokestack, or selectively destroyingviruses, either in vivo or in vitro. Still other embodiments includeselective repair of biomolecules, e.g., repair of thymine dimers orbreaks in the DNA molecule. Unbound base pairs could be specificallyexcited, or DNA could even be intentionally further damaged in a wayselected to trigger the body's own DNA repair mechanism.

An arrangement of inputs that form a score may be analogized to amusical score to aid in understanding some of the aspects. For example,in one approach a score specifies a set of discrete energy inputs, thatmay be in sequential, parallel, or other arrangements. These inputs maybe specified in terms of frequency, modulation frequency, phase,amplitude, temporal profile, polarization, direction, and/or coherence.The set of energy inputs may be played in the form of a “melody” (inwhich each energy input ends before or as the next begins), in the formof a “chord” (in which all the energy inputs begin and end together), orin a more complex structure, which may include one or more overlappingenergy inputs. In addition, the specifications for frequency, modulationfrequency, phase, amplitude, polarization, direction, and/or coherencemay change over the duration of an energy input. In some embodiments,the energy inputs are electromagnetic beams, such as infrared, visibleor ultraviolet beams. The electromagnetic beams may be frequency, phase,amplitude, polarization, pulse width, or otherwise modulated. Suchmodulation may be applied to the base frequency of the electromagneticbeam or may be applied to a beam envelope. In another approach that maybe applied independently or in conjunction with the previously describedapproaches, two or more beams may provide more flexibility in supplyingenergy to a selected location, locations, or structures, at frequencies,spatial selectivities, or other parameters, than single sourceapproaches. In one exemplary approach pairs (or larger sets) of inputscan produce beat frequencies, harmonics, interference patterns, or otherconfigurations. In some such configurations and/or combinations, theenergy inputs may have frequencies differing from the resonantfrequencies of the resonant structures, and yet interact appropriatelywith the molecules.

While the previously described approaches have been exemplified in termsof additive combinations of energy inputs, in some embodiments, aportion of the series of energy inputs may interact with structures tonegate, e.g., by damping or cancellation, rather than enhance,vibrations or other interactions with certain resonant structures.Alternatively or in addition, a structure to which it is desired not totransfer energy may be “deactivated” before, or together with, applyingan energy input. For example, the response of the structure may be“deactivated” or otherwise reduced by temporarily bonding it to anotherstructure that changes its resonant frequency or absorbs vibrationalenergy. In other approaches, locally heating the structure, applying amagnetic or electric field, or applying a local or vector stress orpressure, or otherwise interacting with the structure can change itsresonance, or otherwise reduce its response.

When an application of a score involves affecting compositions in amedium (such as but not limited to living tissue), the score may includeelectromagnetic energy inputs in frequency ranges that penetrate themedium. For example, where a material is contained within a container,the frequencies may be selected where the container is transmissive,yet, the material is responsive. If desired, suitable modulation or beatfrequencies may then be used to resonate the resonant structures of thecomposition.

A schematic of a four-note score illustrating these changes is shown inFIG. 2. Energy inputs I₁ and I₂ overlap in time, with I₁ beginningbefore I₂ begins and ending before I₂ ends. I₁ has a decreasingamplitude with time, while the amplitude of I₂ is substantiallyconstant. I₃ and I₄ begin at substantially the same time, but I₃terminates before I₄. The amplitude of I₃ increases with time whilemaintaining a constant frequency, while the amplitude of I₄ staysconstant with time while the frequency decreases. Phase, polarization,direction, and coherence are not specified in FIG. 2, but each of theseproperties may similarly change with time within a single energy input,or differ from one energy input to another. In particular, phase controlbetween multiple beams may provide spatial, temporal, or otherspecificity that can provide selectivity in resonating only certainstructures within a molecule or in targeting molecules having a certainorientation or position. Morevoer, polarization of the energy inputs maybe useful in distinguishing molecules on the basis of chirality, forexample to excite only molecules having a desired chirality. One skilledin the art will recognize that other combinations, including morecomplex energy inputs may be implemented. For example, frequency andamplitude of an energy input may both be varied. As another example, thefrequency and/or amplitude of an energy input may be increased duringone time interval and decreased during another. As still anotherexample, an energy input may be “chopped” to provide a sequence ofenergy input components. Several other approaches to varying amplitude,frequency, duration or other characteristics of the energy inputs mayalso be implemented according to design and response characteristics ofa given application.

In the specific exemplary case where the score is targeted to a specificmolecule (such as a biomolecule or macromolecule) or a set of molecules,the energy inputs of the score will generally correspond to enoughresonant structures in the target molecule to distinguish it from othermolecules in its environment (as discussed above, the energy inputs may,but need not, have the same frequencies as the resonant structures towhich they correspond). Since most or all of the energy inputs willresonate the target molecule, while only a subset of the energy inputswill resonate other molecules sharing some but not all of the resonantstructures of the target, the target will absorb enough energy from thescore to distinguish it. This effect may cause, for example, localheating in the area of the target molecule, breaking one or more bondsin or to the target molecule, or changing a kinetic parameter of areaction involving the molecule.

In many cases, characteristics of systems including one or more atomsand corresponding bonds may be considered independently. In otherapplications, it may be appropriate to analyze, compensate for, adjustfor, or otherwise consider shifts or changes in characteristics of afirst system including one or more atoms responsive to interaction witha second system having one or more atoms or of energy input to the firstsystem of one or more atoms.

For example, one can identify shifts in the resonant longitudinalvibrational frequency of one or more atomic bonds as a result of opticalpower input, as described in for example, in Andrews and Crisp,“Laser-Induced Vibrational Frequency Shift,” bearing a date of 25 Feb.2005, which is incorporated by reference herein and is appended hereto.This effect may be used to tailor the transfer of energy to a molecule,by adjusting the excitation frequency to match the shift as thevibration increases.

FIG. 3 illustrates how the frequency of one resonant structure may shiftas a nearby resonant structure is excited. When inputs R₁ and R₂ areseparately applied (solid lines), they resonate structures atfrequencies f₁ and f₂. However, when the structures are coupled in aparticular composition, the application of input R₁ may shift theresonant frequency f₂ to f₂′. Thus, that composition may be moreefficiently excited by resonating with input R₁ and an input R₂′ that isfrequency shifted relative to input R₂. In a similar approach, thefrequency of one resonant structure may shift as the resonant structureis subjected to other influences, such as temperature changes. Theenergy inputs may be varied to accommodate such variations in a similarfashion.

FIG. 4 illustrates schematically how a score may be used to selectivelyexcite a particular molecule sufficiently to break a bond, which candestroy the molecule. As shown, inputs I₁, I₂, I₃, and I₄ are applied tothe composition in a sequence which may include temporal overlap. InputI₁ excites a first resonant structure, adding energy to the molecule. Aseach additional input excites its own respective resonant structure inthe molecule, the energy added increases as shown, until I₄ drives thevibration past the breaking strength for a bond (shown schematically asdashed line 10). Each of the individual inputs may be insufficient aloneto destroy the molecule, but acting in concert, they do. Where theenergy to break the bond is higher than that which would be provided bya combination of less than all four inputs (assuming no increase in theamplitudes of the individual inputs), only molecules having the fourresonant structures in sufficient proximity will experience the breakingof the bond (it will of course be understood that this technique is notlimited to scores specifying exactly four inputs, but that it may beapplied with as few as two inputs or as many as appropriate to achievethe final effect).

This selectivity can be further enhanced by exploiting frequency shiftsas discussed above, to more selectively interact with molecules whoseresonant structures are responsive to the shifted frequencies. Note thatthe effect of combining respective inputs to provide cumulative energyinput is not limited to breaking bonds as presented in this exemplaryembodiment. For example, the approach described herein may also be usedto alter kinetic parameters or to achieve any other desired chemical,physical or other effect.

FIG. 5 illustrates another scenario in which a bond in a molecule havinga substantially linear portion can be excited to breakage. As shown, themolecule includes a chain of atoms A, B, C, D, E, and F. Initially,respective inputs excite the A-B and E-F, causing secondary excitationand/or frequency shifting of adjacent bonds B-C and D-E. Subsequentinputs excite the adjacent bonds B-C and D-E. The excitations of thebonds B-C and D-E causes a further excitation and/or frequency shift ofcenter bond C-D. The cumulative effect of the inputs to bonds A-B, B-C,D-E, E-F excites bond C-D. In some applications, the cumulativeexcitation of bond C-D from the adjacent bonds is sufficient to breakbond C-D. In some cases, additional excitation directed at bond C-D iscombined with the cumulative excitation of bond C-D from the adjacentbond to produce the intended result, such as severing the C-D bond. Ofcourse, the technique is not limited to molecules having the simplelinear structure shown in FIG. 5, but can be applied to any compositionin which two sequences of resonant structures can be identified thatlead to a common center.

In addition, it may not be necessary to actively excite all of the bondsor other structures along the path to the common center. For example,the excitation of the A-B and E-F bonds shown in FIG. 5 may besufficient to cause secondary excitation of the B-C and/or D-E bondswithout additional energy inputs. In this way, energy inputs targeted toremote structures A-B and E-F may propagate along the molecule, meetingto cause a desired effect at targeted center structure C-D. In suchembodiments, the targeted bond need not be exactly at the midpointbetween the remote structures as shown in FIG. 5; the timing of theexcitation of the remote structures may be adjusted to determine adesired “meeting point” for the propagated excitations.

Moreover, depending upon the amount of energy and the particularcharacteristics of the bonds and atoms, the inputs to excite the variousbonds may be applied substantially simultaneously, may be applied attimes that only overlap partially, or that are non-overlapping. Further,certain resonant structures may be “rung up” and “rung down” in amulti-step process by applying excitation and anti-excitation (e.g.,damping or canceling) energy inputs as discussed above. Controlling therelative timing, intensities, orientations, or other characteristics ofthe plurality of energy inputs according to the ring up response, orother transient response characteristics of the resonant structures canincrease the selectivity, efficiency, or other parameters of energytransfers to or from the resonant structures. Such techniques may alsobe useful to create intermediate structures or effects, analogous to thecreation of intermediate structures in a multi-step chemical synthesisor reaction.

For certain compositions, transfer of energy to the resonant structureswill be a function of the orientation of the resonant structure relativeto the direction of the energy input. FIGS. 6 and 7 illustrate twoembodiments that allow this relative orientation effect to be exploited.

In FIG. 6, three energy inputs I₁, I₂, and I₃ from different directionsconverge at a target location (voxel) within a medium containingdirection-dependent resonant structures. Since the energy inputs comefrom different directions, they each affect resonant structures in adifferent orientation. By selecting an appropriate number of energyinputs in different directions, an arbitrarily high percentage of thetarget resonant structures can be affected by the beams. These energyinputs need not be simultaneously applied from separate sources, asshown in FIG. 6; they may also be applied by a single source, whereeither the source or the target material is rotated in order to changethe effective direction of the energy input, or where the single sourceis redirected by means of reflectors, beam splitters, optical fibers,applied fields, or other known energy directing elements. In addition,the energy input(s) may be scanned relative to the material to affect aplurality of voxels within the material. Further, multiple energy inputsneed not always intersect as shown in FIG. 6, but may be independentlydirected according to the needs of a particular application. Theplurality of energy inputs shown may have either the same or differingfrequency, phase, amplitude, temporal profile, polarization, and/orcoherence, depending on the needs of the particular application.Multiple energy inputs may also be used even withnon-direction-dependent structures, for example in order to overcomescattering within the medium. Where a plurality of inputs excite a givenvoxel, from differing locations or orientations, the excitation in thevoxel may exceed that of locations outside of the voxel, therebyallowing selective excitation of the voxel at a selected level.

In another aspect, shown in FIG. 7, an additional influence canactivate, orient, or otherwise influence resonant structures 20 tointeract appropriately with resonant inputs. In the exemplary approachof FIG. 7, an electric field applied to the target material alignsresonant structures 20 prior to application of an energy input. Whilethe exemplary embodiment employs an electric field to influence theresonant structures, any applied field that tends to affect theinteraction of the resonant structures with the energy input may beapplied, including without limitation a magnetic field, an appliedmechanical stress, a lowered or elevated temperature or pressure, aphase change, introduction of an adsorbing surface or catalyst, or theapplication of another energy input. Rotating a number of resonantstructures into a known orientation may allow more efficient excitation,a simpler configuration, or a reduced number of energy inputs (e.g.,only I₁ as shown in FIG. 7) to resonate the resonant structuresappropriately. As previously described in reference to FIG. 6, theapplied energy input(s) may be scanned, rotated, or otherwise adjustedrelative to the material. In addition, the applied field itself may bescanned, rotated, or otherwise adjusted relative to the target, forexample by movement or rotation of the field or by movement or rotationof the target.

FIG. 8 shows schematically a method of applying energy. A suitable scoreis selected by any of a variety of methods, some of which are detailedherein, and then energy is applied to a target in conformance with thescore. The score specifies a plurality of energy inputs that apply theenergy. The energy may, for example, be applied in the form of one ormore electromagnetic beam(s), in which case the score may specifyfrequency, modulation frequency, phase, amplitude, temporal profile,polarization, and/or coherence for the beam(s).

FIG. 9 shows schematically a device for applying energy in accordancewith a score. Interpreter 30 accepts a score which specifies a pluralityof energy inputs. The interpreter may include an electronic controller31 that can receive the score from a source 33, such as a database orlibrary (e.g., the library described below with reference to FIG. 13), afeedback system (e.g., the feedback system described below withreference to FIG. 10), a score generator (e.g., the modeling tooldescribed below with reference to FIG. 11) or other source of a score.The source 33 may be within or integral to the interpreter 30, orexternal to or remote from the interpreter 30.

Additionally, the source 33 may be located proximate to the interpreter,may be separate from the interpreter, or may be distributed. In oneexample, the source may be implemented logic or circuitry that alsoincludes logic or circuitry that forms a part of the interpreter. In oneexample of a distributed source, a remotely located component, such as acentral database, provides information relative to the score that isconverted by a local component, such as a computer, to data appropriatefor use by the interpreter 30. Alternatively, the information relativeto the score may be converted by the electronic controller 31 within theinterpreter, or may be provided to the interpreter in a format notrequiring conversion.

The energy application device may also include a score locationcomponent (not shown), which may select a score for conversion by theinterpreter, for example from a library of scores, or a score inputcomponent (not shown) that accepts a score from a user. In otherembodiments, an input component may accept an input composition orstructure (e.g., from a user), and return a score that has an effect onthe accepted composition or structure or on a portion of the acceptedcomposition or structure, to the interpreter. In some embodiments, theinput component may then present the returned score to the user forapproval before passing it to the interpreter.

The presented returned score may be represented to the user visually ina variety of manners. For example, the score may be presentedgraphically as a spectrographic representation, a dynamic model, aspreadsheet, or other user perceivable representation. Therepresentation may also include additional information, such as a visualrepresentation of a different score. Such presentation may provide avisually perceivable contrast to the user, for example by highlightingenergy inputs that are added, subtracted, or modified in one scorerelative to another.

In another approach, the score may be presented audibly to the user. Insuch a case, each note of the score may be converted to a correspondingaudible note that the user can detect. In some cases, it may beappropriate for the correspondence between the notes of the score andthe presented audible notes to be established according to astandardized protocol. This can aid a user in detecting patterns anddeviations from such patterns by identifying “off-key” audible notes. Inone such protocol, a range of frequencies of the input energies can mapto a range of audible frequencies, in a linear, logarithmic, or othermapping, such that increases in the input energy frequency can berepresented as increases in the audible frequency. Moreover, intensitiesor amplitudes may also be mapped to provide audible indications of theamplitudes of the notes in the score. One skilled in the art willrecognize that other types of mapping or correlations may also beapplied. For example, the frequency mapping may be inverted, the variousinput frequencies may be mapped into subsets of frequencies (e.g.,ranges of input frequencies mapped to selected octaves of the audiblefrequencies), or other types of audible presentations may be developed.Further, in addition to, or in lieu of, a signal audible to a user, thescore may be mapped to an acoustic signal detectible by an acousticreceiver that can act as a monitor of the score components.

In another aspect, the information representing the score may becompressed or encrypted according to known techniques. The interpretermay accept an authorization (e.g., a decryption key or authorizationcode) or may decompress the information to produce a more completerepresentation of the score before continuing the process, as describedbelow.

The interpreter converts the score into appropriate control instructionsfor an energy input device 32 (e.g., a laser). The energy input deviceapplies the energy inputs 34 to a target 36. The energy input device mayapply energy using either a single or a plurality of beams (e.g., anarray of lasers). The energy input device may further comprise optionalelements 38 that direct and/or modify the beam (e.g., reflectors,polarizers, optical fibers, lenses, and/or other optical couplingelements).

FIG. 10 shows schematically a device with optional monitoring andfeedback control for score application. A score generator 40 (which mayinclude, for example and without limitation, a database of scores, amolecular modeling device that determines resonant frequencies, adatabase of spectrographs, or another source of scores as describedherein) provides a score to an energy input component 42. The energyinput component applies energy inputs to a target 44 as specified by thescore. In addition, a monitor 46 may observe the effect on the target ofthe applied energy inputs. In embodiments in which a monitor is present,it may optionally provide feedback to the score generator, which maythen provide a new or adjusted score to the energy input component inresponse to the observations of the monitor. The monitor may be of atype that identifies energy levels, kinetic effects, structuralvariations, chemical variations or any other appropriate variation inthe target 44. For example, thermal imaging can provide an indication ofthermal buildup in the target. In another example, an optical beam maypass through or be reflected from the target. As is known, in somematerials, the optical transmission or reflection properties (e.g.,index or refraction, diffraction phenomena, or absorption) can be afunction of stresses, thermal effects, or other effects that may beinduced by the input component 42; the monitor uses the optical beam todetect these changed properties, revealing the effects induced by theinput component.

In biological applications, scores may be used for diagnostic and/ortherapeutic purposes. For example, in embodiments involving thetreatment of blood, a monitoring device may be placed over a bloodvessel (e.g., in the wrist or on the earlobe), continually monitoringand/or altering blood chemistry as blood flows close to the skin.Alternatively, a fiber optic cable or other physical device for energytransmission may deliver energy impulses deeper into the body. In eithercase, a substantial portion, or even all, of the entire volume of bloodof a patient can be treated in a relatively short amount of time as theblood circulates through a targeted vessel. The monitoring device may,for example, observe and/or chemically modify proteins in the blood. Inanother embodiment, the monitoring device may continuously monitor bloodcomponents such as sugars, triglycerides, or cholesterol, and optionallymoderate their levels if they pass a threshold.

FIG. 11 shows schematically an apparatus for generating scores based oncomputational modeling of resonant structures. A modeling tool 50generates a model of a structure (e.g., a molecular model of a chemicalcomposition, or a quantum mechanical model of the energy levels of aquantum dot) in order to determine its predicted resonances. A scoregenerator 52 then incorporates the predicted resonances into a score.The generated score may be passed to an energy input instrument.

FIG. 12 shows schematically a system for introducing a chemical agentinto a medium, which may in some embodiments be used for therapeuticpurposes. As shown, the chemical agent comprises a composition 60 boundto an optional carrier 62, which is located within a medium 64. Energyinput device 66 applies a score to the medium. In some embodiments, thisscore is selected to sever the bond between the composition and thecarrier, thereby releasing the composition into the medium. In otherembodiments, the applied score activates the composition directly, forexample by breaking one or more bonds of the composition, ablatingmaterial surrounding the composition, heating material surrounding thecomposition, or reacting with material surrounding the composition. Insome embodiments, these techniques may be used to deliver a catalyst orother chemical agent to difficult-to-reach areas. For example, acleaning or recharging agent could be dispersed throughout a watertreatment system in an inert form, and then rendered active byapplication of a score to the whole system. Such an embodiment may insome cases allow more uniform application of the cleaning or rechargingagent, particularly in high-surface-area systems where a reactive agentmay be difficult to disperse throughout the system.

For use in vivo, the optional carrier or the composition may have anaffinity to a selected substance or tissue, which forms the medium ofFIG. 12. The optional carrier or the composition may be placed directlyin a particular tissue (e.g., by injection into the tissue), or may beintroduced into the body and allowed to accumulate at the selectedtissue. For example, an iodine-containing composition may be introducedinto the body orally or by injection into the bloodstream, and allowedto accumulate in the thyroid gland. A score comprising infrared energyinputs (to which the body is substantially transparent) may then be usedto heat the iodine-containing composition, thereby ablating a tumorand/or a portion of the thyroid gland itself. Other compositions orcarriers may similarly be chosen to accumulate in other tissues (e.g.,calcium in the bones or teeth or organic compounds in the liver), andthen activated by application of a score (e.g., to release a stimulantto cell division and/or growth). Inhaled compositions, optionally boundto fine carriers, may be distributed to the alveoli for treatment of thelungs.

FIG. 13 shows schematically a library of excitation energyspecifications, comprising a structured data repository 70 comprising aplurality of score records. Each score record includes descriptors for aplurality of energy inputs, a descriptor for associated composition(s)affected by the plurality of energy inputs, and optionally a descriptordescribing the effect of the plurality of energy inputs on thecomposition. The energy input descriptors describe at least one offrequency, modulation frequency, phase, amplitude, temporal profile,polarization and direction for each energy input. The library may alsoinclude additional features such as a search engine 72, an inputcomponent 74, and/or an output component 76. If provided, the outputcomponent may provide a user with a score record for download, forexample so that it may be used to direct an energy input device to playthe score in order to affect the associated composition. The library maybe used to screen for a composition, by accessing the library to locatea score record for the composition, applying the energy inputs describedby the energy input descriptors of the score record to a medium, andobserving the medium for reaction of the composition to the appliedinputs. The library may also be used to excite the composition, byaccessing the library to locate a score record for the composition andapplying the energy inputs described by the score record to thecomposition (e.g., to destroy the composition). Alternatively, theselected score record may comprise a descriptor of a composition sharinga functional group with the composition to be excited.

Those having skill in the art will recognize that the state of the artof circuit design has progressed to the point where there is typicallylittle distinction left between hardware and software implementations ofaspects of systems. The use of hardware or software is generally adesign choice representing tradeoffs between cost, efficiency,flexibility, and other implementation considerations. Those having skillin the art will appreciate that there are various vehicles by whichprocesses, systems and/or other technologies involving the use of logicand/or circuits can be effected (e.g., hardware, software, and/orfirmware), and that the preferred vehicle will vary with the context inwhich the processes, systems and/or other technologies are deployed. Forexample, if an implementer determines that speed is paramount, theimplementer may opt for a mainly hardware and/or firmware vehicle.Alternatively, if flexibility is paramount, the implementer may opt fora mainly software implementation. In these or other situations, theimplementer may also opt for some combination of hardware, software,and/or firmware. Hence, there are several possible vehicles by which theprocesses, devices and/or other technologies involving logic and/orcircuits described herein may be effected, none of which is inherentlysuperior to the other. Those skilled in the art will recognize thatoptical aspects of implementations may require optically-orientedhardware, software, and or firmware.

The foregoing detailed description has set forth various embodiments,some of which incorporate logic and/or circuits, via the use of blockdiagrams, flow diagrams, operation diagrams, flowcharts, illustrations,and/or examples. Insofar as such block diagrams, operation diagrams,flowcharts, illustrations, and/or examples contain one or morefunctions, operations, or data structures to be performed, manipulated,or stored by logic and/or circuits, it will be understood by thosewithin the art that each such logic and/or circuit can be embodied,individually and/or collectively, by a wide range of hardware, software,firmware, or virtually any combination thereof. For example, someembodiments of the subject matter described herein may be implementedvia Application Specific Integrated Circuits (ASICs), Field ProgrammableGate Arrays (FPGAs), digital signal processors (DSPs), or otherintegrated formats. However, those skilled in the art will recognizethat other embodiments disclosed herein can be equivalently implementedin whole or in part in standard integrated circuits, as one or morecomputer programs running on one or more computers (e.g., as one or moreprograms running on one or more computer systems), as one or moreprograms running on one or more processors (e.g., as one or moreprograms running on one or more microprocessors), as firmware, as analogcircuitry, or as virtually any combination thereof, and that designingthe circuitry and/or writing the code for the software and or firmwarewould be well within the skill of one of skill in the art in light ofthis disclosure. In addition, those skilled in the art will appreciatethat the operations, functions, and data (e.g., scores) described hereinare capable of being distributed or stored in a variety of signalbearing media. Examples of a signal bearing media include, but are notlimited to, recordable type media such as floppy disks, hard diskdrives, CD ROMs, digital tape, and computer memory, and transmissiontype media such as digital and analog communication links using TDM orIP based communication links (e.g., packet links). The choice of signalbearing media will generally be a design choice representing tradeoffsbetween cost, efficiency, flexibility, and other implementationconsiderations in a particular context, and none of these signal bearingmedia is inherently superior to the other.

1. A method for applying energy to a selected group of proximate atoms within a medium, the method comprising: selecting a score specifying a series of at least four differing energy inputs, the differing energy inputs of the specified series selected to resonate each resonant structure of a plurality of resonant structures among the group of proximate atoms, wherein at least one resonant structure among the plurality of resonant structures includes a bond; and applying the series of differing energy inputs specified by the score to the medium.
 2. The method of claim 1, wherein the score is selected such that the applied series of differing energy inputs has a physical effect selected from the group consisting of: transferring substantially more energy to the at least a portion of the group of proximate atoms than to atoms in the medium that are not part of the group of proximate atoms; breaking a predetermined bond between two members of the group of proximate atoms; and changing a kinetic parameter of a reaction involving a member of the group of proximate atoms.
 3. The method of claim 1, wherein transfer of energy to the medium is predominantly through resonant excitation of the plurality of resonant structures.
 4. The method of claim 1, wherein the score specifies application of an electromagnetic beam as an energy input.
 5. The method of claim 4, wherein the electromagnetic beam has at least one characteristic selected from the group consisting of: a selected set of frequencies; a selected set of modulation frequencies; a selected set of phases; a selected set of amplitudes; a selected temporal profile; a selected set of polarizations; and a selected direction.
 6. The method of claim 5, wherein the electromagnetic beam is coherent.
 7. The method of claim 5, wherein the selected set of frequencies comprises at least two frequencies, and wherein the at least two frequencies have differing amplitudes.
 8. The method of claim 5, wherein the selected set of modulation frequencies comprises at least two frequencies, and wherein the at least two frequencies have differing amplitudes.
 9. The method of claim 4, further comprising scanning the electromagnetic beam.
 10. The method of claim 5, wherein the selected set of modulation frequencies comprises a plurality of local maxima.
 11. The method of claim 4, wherein the electromagnetic beam is an infrared beam.
 12. The method of claim 4, wherein the electromagnetic beam is amplitude modulated.
 13. The method of claim 4, wherein the electromagnetic beam is frequency modulated.
 14. The method of claim 1, wherein at least one energy input comprises a plurality of electromagnetic beams.
 15. The method of claim 14, wherein the plurality of electromagnetic beams intersect at a target location.
 16. The method of claim 1, further comprising applying a field to the medium, wherein the field acts to preferentially orient at least a portion of the group of proximate atoms.
 17. The method of claim 16, wherein the field is selected from the group consisting of an electric field, a magnetic field, an electromagnetic field, a mechanical stress, a mechanical strain, a lowered or elevated temperature, a lowered or elevated pressure, a phase change, an adsorbing surface, a catalyst, an energy input, and combinations thereof.
 18. The method of claim 1, wherein: the plurality of resonant structures are in an arrangement having two end resonant structures and a center resonant structure; and the plurality of resonant structures are resonated in a sequence beginning from the two end resonant structures and progressing towards the center resonant structure.
 19. The method of claim 18, wherein resonance of the center structure breaks a predetermined bond between two members of the group of proximate atoms.
 20. The method of claim 18, wherein the plurality of resonant structures are resonated in a temporally overlapping sequence.
 21. The method of claim 18, wherein the group of proximate atoms undergoes a physical effect upon resonance of the center structure.
 22. The method of claim 1, wherein the series of differing energy inputs are applied in a temporally overlapping fashion.
 23. The method of claim 1, wherein the group of proximate atoms forms at least a portion of a molecule.
 24. The method of claim 23, wherein the molecule is a biomolecule.
 25. The method of claim 24, wherein the biomolecule is a protein or a nucleotide.
 26. The method of claim 1, wherein the group of proximate atoms forms at least a portion of a crystal.
 27. The method of claim 1, wherein the group of proximate atoms forms at least a portion of a complex of molecules.
 28. The method of claim 1, wherein no two members of the group of proximate atoms are separated by a distance of more than 300Å.
 29. The method of claim 1, wherein all members of the group of proximate atoms are connected directly or indirectly by bonds between the atoms.
 30. The method of claim 1, wherein the plurality of resonant structures comprises a longitudinal vibrational mode of a bond.
 31. The method of claim 1, wherein the plurality of resonant structures comprises a bending mode of two bonds to a member of the group of proximate atoms.
 32. The method of claim 1, wherein the plurality of resonant structures comprises a squashing mode of a plurality of bonds between members of the group of proximate atoms. 